Variant report

Variant	rs3762452
Chromosome Location	chr1:211276828-211276829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:211276107..211279253-chr1:211280541..211283887,3	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12735839	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12750065	0.87[ASN][1000 genomes]
rs12755446	0.87[ASN][1000 genomes]
rs12760898	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17188839	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17188846	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17188881	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17267414	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17267421	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17267428	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17267442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34247884	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34403324	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35035396	0.85[EUR][1000 genomes]
rs35385507	0.87[ASN][1000 genomes]
rs35593738	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35664000	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35714691	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35829564	0.84[ASN][1000 genomes]
rs35957403	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36005892	0.83[ASN][1000 genomes]
rs36115666	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828159	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4326688	0.87[ASN][1000 genomes]
rs4612687	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59200985	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662529	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6679835	0.87[ASN][1000 genomes]
rs71638196	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs71638198	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71638199	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512567	0.87[ASN][1000 genomes]
rs7512644	0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3762452	C1orf74	cis	parietal	SCAN
rs3762452	KCNH1	cis	cerebellum	SCAN
rs3762452	GLE1	trans	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211256400-211285400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:211256800-211277000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:211256800-211282400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:211264400-211277400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:211265400-211277200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:211266400-211280200	Weak transcription	Pancreas	Pancrea
7	chr1:211269800-211278600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:211271400-211286000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:211273000-211278000	Weak transcription	Brain Hippocampus Middle	brain
10	chr1:211273200-211277800	Strong transcription	HSMMtube	muscle
11	chr1:211273200-211281200	Weak transcription	A549	lung
12	chr1:211273200-211282400	Strong transcription	HSMM	muscle
13	chr1:211276600-211277400	Enhancers	Brain Angular Gyrus	brain
14	chr1:211276600-211278000	Enhancers	Brain Substantia Nigra	brain
15	chr1:211276600-211278400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:211276800-211278800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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